Journal Articles

In Preparation

63. Ibrahim Ahmed, Peter Witbooi, Eileen Hoal and Alan Christoffels (2014). Prediction of human-Mycobacterium tuberculosis protein-protein interactions using a multi-layer neural network. Submitted

62. Mmakamohelo Direko, Nico Gey van Pittius, Rob Warren, Paul van Helden and Alan Christoffels. Genome analysis of next generation sequencing data for the Mycobacterium orygis; species of the Mycobacterium tuberculosis complex. In prep

61. Sarah Mwangi, Mushal Ali, Peter van Heusden and Alan Christoffels. GmPromDB: A database of Glossina morsitans promoters. In prep.

60. Stanley Kimbung Mbandi, Lizex Husselmann, Uljana Hesse, Joseph Mafofo, D.Jasper G. Rees and Alan Christoffels. Identification of scab putative effector candidates and apple resistance genes: a comparison of Venturia inaequalis trancriptomes. Submitted BMC Genomics.

59. Mushal Ali Hiba Abdallah, Lizette Koekemoer and Alan Christoffels. Insectar: predicting functional targets of Anopheles miRNA. Submitted


58. Ruben Cloete ,Wisdom Akurugu, Cedric Werely, Paul van Helden and Alan Christoffels (2017). Predicting the effects of nucleotide variation on the structure and function of human arylamine N-acetyltransferase 1 in a South African population. Accepted Journal of Molecular Graphics

57. Samuel Kyobe, Henry Musinguzi, Moses Joloba, Akin Abayomi, Carmen Swanepoel, Alashle Abimiku, Talishiea Croxton, Alan Christoffels, Elizabeth Mayne, Newton Lwanga, Fred Katabazi, Dafala Kezimbira, Mukthar Kader, Garth Swartz, Edgar Kigozi, Misaki Wayengera, Lizelle van Zyl (2017). Selecting a laboratory information management system for biorepositories in low and middle income countries: The H3Africa Experience. Biopreservation and Biobanking 15 (2): 112-115 DOI:10.1089/bio.2017.0006

56. Hocine Bendou, Lunga Sizani, Tim Reid, Carmen Swanepoel, Toluwaleke Ademuyiwa, Akin Abyaomi, Roxana Merino-Martinez, Heimo Meuller and Alan Christoffels (2017). B3aobab LIMS: Development of an opensource LIMS for Biobanking. Biopreservation and Biobanking.15 (2): 116-120 DOI:10.1089/bio.2017.0014

55. Christine Beiswanger, Alash’le Abimiku, Nadia Carstens, Alan Christoffels, Jantina de Vries, Audrey Duncanson, Morne du Plessis, Maria Giovanni, Katherine Littler, Nicola Mulder, Jennifer Troyer, Louise Wideroff, H3Africa Data and Biospecimen Sharing Organizing Committee (2017). Accessing Biospecimens from the H3Africa Consortium”. Biopreservation and Biobanking. 15 (2): 95-98 DOI:10.1089/bio.2017.0008


54. Mushal Allam, Belinda L Spillings, Hiba Abdallah, Darlington Mapiye, Lizette Koekemoer and Alan Christoffels (2016). Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing. Malaria Journal. 15:542 DOI 10.1186/s12936-016-1591-0 [PDF]

53. Werner Veldsman and Alan Christoffels (2016). SNiPhunter. A SNP based search engine. Data, 1, 17 doi:10.3390/data1030017

52. Darlington Mapiye, Alan Christoffels and Junaid Gamieldien (2016). Identification of phenotype-relevant differentially expressed genes in breast cancer demonstrates enhanced quantile discretization protocol’s utility in multi-platform microarray data integration. Journal of Bioinformatics and Computational Biology 14(6): DOI:10.1142/S0219720016500220 .

51. Tomas Klingstrom, Maimuna Mendy, Dominique Meunier, Anouk Berger, Jane Reichel, Alan Christoffels, Hocine Bendou, Carmen Swanepoel, Lemoene Smit, Campbell Mckellar-Basset, Erik Bongcam-Rudloff, Jonas Soderberg,Roxana Merino-Martinez, Suyesh Amatya, Absolomon Kihara, Steve Kemp, Robert Reihs and Heimo Muller. Supporting the development of biobanks in Low and Medium Income Countries. IST-Africa 2016 Conference Proceedings. Paul Cunningham and Miriam Cunningham (Eds) IIMC International Information Management Corporation. ISBN: 978-1-905824-55-7

50. Zahra Jalali Sefid Dashti, Junaid Gamieldien and Alan Christoffels. Computational characterization of iron metabolism in Glossina morsitans: IRE stem-loops. BMC Genomics 17:561 (2016) [PDF]

49. Vij Shubha, Kuhl H., Kuznetsova I.S., Komissarov A et al. (2016) Chromosome-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding. 12(4): e1005954. Doi:10.1371/journal.pgen.100595

48. Mulder NJ, Christoffels A, de Oliveira T, Gamieldien J, Hazelhurst S, et al.(2016)The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt. PLoS computational biology. 2016; 12(2):e1004395.

47 Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, et al.(2016) H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa.Genome research. 2016; 26(2):271-7.

46 Macharia R, Mireji P, Murungi E, Murilla G, Christoffels A, Serap Aksoy and Daniel Masiga.(2016)Genome-Wide Comparative Analysis of Chemosensory Gene Families in Five Tsetse Fly Species.PLoS neglected tropical diseases. 2016; 10(2):e0004421.

45. Samuel Egieyeh, James Syce, Sarel F. Malan, Alan Christoffels. Prioritisation of anti-alarial hits from nature: chemo-informatic profiling of natural products with in vitro antiplasmodial activities and currently registered anti-malarial drugs. Molecules (2016)15:50

44. Samuel Egieyeh, James Syce, Alan Christoffels, Sarel F. Malan. Exploration of scaffolds from natural products with antiplasmodial activities, currently registered anti-malarial drugs and public malarial screen data. Malaria Journal. (2016) 21(1): 104

43. Cloete R, Oppon E, Marti-Renom M, Murungi E, Schubert WD, Christoffels A.(2016) Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis. BMC Bioinformatics (2016); 17:75 [PDF Download]


41 Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, et al.(2015) GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training. PLoS computational biology. 2015; 11(4):e1004143.

40. Sarah Mwangi, Mushal Ali, Geoffrey Attardo, Serap Aksoy, Yutaka Suzuki and Alan Christoffels. Analysis of the core promoter architecture of the blood feeding disease vector, Glossina morsitans using TSS-seq. BMC Genomics (2015), 16:722

39. Mbandi Stanley Kimbung , Uljana Hesse, Peter van Heusden, Alan Christoffels. Inferring bona fide transcripts in RNA-Seq derived-transcriptome assemblies of non-model species (2015).BMC Bioinformatics. 16: 58 DOI: 10.1186/s12859-015-0492-5

38. Celia van der Merwe, Zahra Jalali Sefid Dashti, Alan Christoffels, Ben Loos, Soraya Bardien (2015). Evidence for a common biological pathway linking three Parkinson’s Disease causing genes: Parkin, PINK1 and DJ-1. European Journal of Neuroscience. 41(9): DOI: 10.1111/ejn.12872


37. Edwin Murungi, Henry M. Kariithi, Vincent Adunga, Meshack Obonyo and Alan Christoffels (2014). Evolution and Structural analyses of Glossina morsitans Tetraspanins. Insects. 5: 885-908, doi:10.3390/insects5040885

36. Daniel Masiga, George Obiero, Rosaline Macharia, Paul Mireji and Alan Christoffels (2014). Chemosensory receptors in tsetse flies provide link between chemical and behavioural ecology. Trends in Parasitology. 30(9): 426-428. DOI: 10.1016/

35. Barbara Picone and Alan Christoffels. Adaptive and molecular evolution of receptor genes implicated in susceptibility to Tuberculosis (2014). International Journal of Genetics and Genomics. 2(4): 57-61. doi: 10.11648/j.ijgg.20140204.12

34. Alan Christoffels, Dan Masiga, Mathew Berriman, Mike Lehane, Yeya Toure and Serap Aksoy (2014). International Glossina Genome Initiative 2004-2014: a driver for post-genomic era research on the African continent. PLoS Negl Trop Dis. 8(8) e3024

33. The H3Africa Consortium (2014). Enabling African Scientists to Engage fully in the Genomic Revolution. Science 344 (6190): 1346-1348

32. International Glossina Genome Initiative (2014). Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. Science 344: 380-386.

31. Stanley Kimbung Mbandi, Uljana Hesse, Jasper Rees and Alan Christoffels (2014). A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads. Front. Genet 5:17. doi:10.3389/fgene.2014.00017.

30. Serap Aksoy, Geoffrey Attardo, Matt Berriman, Alan Christoffels, Mike Lehane, Dan Masiga and Yeya Toure. Human African Trypanosomiasis Research Gets a Boost: Unraveling the Tsetse Genome. PLoS Negl Trop Dis 8(4):e2624. doi:10.1371/journal.pntd.0002624.

29. George Fredrick Obiero, Steven R.G Njanjom, Paul O. Mireji, Alan Christoffels, Hugh Robertson and Daniel K. Masiga (2014). Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans. PLoS Negl Trop Dis. 8(4):e2663. doi: 10.1371/journal.pntd.0002663

28. Harkins, GW., Martin, DP., Christoffels, A. and Varsani A. (2014) Towards inferring the global movement of beak and feather disease virus. Virology 450-451: 24-33. doi: 10.1016/j.virol.2013.11.033.

27. Murungi, E., Adunga, V., Amanda J. O’Reilly, A.J., Field, M.C., and Christoffels, A (2014). Comparative analysis of kinetoplastid SNARE proteins. Parasitology International 63(2): 341-348

26. Rajini Sreenivasan, Junhui Jiang, Xingang Wang, Richard Bartfai, Hsiao Yuen Kwan, Alan Christoffels, and Laszlo Orban (2014). Gonad Differentiation in Zebrafish Is Regulated by the Canonical Wnt Signaling. Biology of Reproduction. 90 (2): 45, 1-10 doi:10.1095/biolreprod.113.110874

25. Barbara Picone, Uljana Hesse, Sumir Panji, Peter van Heusden, Mario Jonas and Alan Christoffels (2014). Taste and Odorant Receptors of the Coelacanth – A Gene Repertoire in Transition. Journal Experimental Zoology (Part B Mol.Dev. Evol) 322(6): 403-414 DOI: 10.1002/jez.b.22531


24. Akin Abayomi, Alan Christoffels, Ravnit Grewal, Locunda A. Karam, Catherine Rossouw, Ciara Staunton, Carmen Swanepoel, Beverley van Rooyen (2013). Challenges of Biobanking in South Africa to facilitate indigenous research in an environment burdened with HIV, TB and emerging non-communicable diseases. Biopreservation and Biobanking 11: 347-354 DOI: 10.1089/bio.2013.0049

23. Chris Amemiya et al (80 authors) (2013). Comparative analysis of the genome of the African coelacanth, Latimeria chalumnae, sheds light on tetrapod evolution. The African Coelacanth provides insights into tetrapod evolution. Nature 496: 311-316


22. Adam Dawe, Aleksandar Radovanovic, Mandeep Kaur, Sunil Sagar, Sundarararajan Seshadri, Ulf Schaefer, Allan Kamau, Alan Christoffels and Vladimir Bajic (2012) DESTAF: A Database of Text-Mined Associations for Reproductive Toxins Potentially Affecting Human Fertility. Reproductive Toxicology 33: 99– 105.

21. Vijayaraghava Sundararajan, Musa Nur Gabere, Ashley Pretorius, Saleem Adam, Alan Christoffels, Minna Lehvaslaiho and Vladimir Bajic (2012). DAMPD: A manually curated antimicrobial peptide database. Nucleic Acids Research. 40(Database issue): D1108-12


20. Vladimir Shulaev, Daniel J Sargent, Ross N Crowhurst, Todd C Mockler, Otto Folkerts, Arthur L Delcher, Pankaj Jaiswal, Keithanne Mockaotis, Aaron Liston, Shrinivasrao P Mane, Paul Burns, Thomas M Davis, Janet P Slovin, Nahla Bassil, Roger P Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R Crastam Roderick V Jensen, Andrew C Allan, Todd P Michael, Joao Carlos Setubal, Jean-Marc Celton, D Jasper G Rees, Kelly P Williams, Sarah H Holt, Juan Jairo Ruiz Rojas, Mithu Chatterjee, Bo Liu, Herman Silva, Lee Meisel, Avital Adato, Sergei A Filichkin, Michela Troggio, Roberto Viola, Tia-Lynn Ashman, Hao Wang, Palitha Dharmawardhana, Justin Elser, Rajani Raja, Henry D Priet, Douglas W Bruant Jr, Samuel E Fox, Scott A Givan, Larry J Wilhelm, Sushma Naithani, Alan Christoffels et al (2011) The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 43: 109-116. Doi:10.1038/ng.740

19. Monique Maqungo; Mandeep Kaur; Samuel K. Kwofie; Aleksandar Radovanovic; Ulf Schaefer; Sebastian Schmeier; Ekow Oppon; Alan Christoffels; Vladimir B. Bajic (2011)
 DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Research 39: D980-D985; doi: 10.1093/nar/gkq849.


18. Jean-Marc Celton, Alan Christoffels, Daniel J Sargent, Xiangming X and David J.G Rees (2010) Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map. BMC Biology. 8:155-8


17. Shu-Ye Jiang, Alan Christoffels, Rengasamy Ramamoorthy and Srinivasan Ramachandran. Expansion mechanisms and functional annotations of hypothetical genes in the rice genome (2009). Plant Physiology. 150: 1997-2008.

16. Magbubah Essack, Aleksandar Radovanovic, Ulf Schaefer, Sebastian Schmeier, Sundararajan V Seshadri, Alan Christoffels, Mandeep Kaur and Vladimir B Bajic (2009) DDEC: Dragon Database of Genes Implicated in Esophageal Cancer. BMC Cancer 9: 219-226.

15. Mandeep Kaur, Aleksandar Radovanovic, Magbubah Essack, Ulf Schaefer, Monique Maqungo, Tracey Kibler, Sebastian Schmeier, Alan Christoffels, Kothandaraman Narasimhan, Mahesh Choolani and Vladimir Bajic (2009). Database for exploration of functional context of genes implicated in ovarian cancer. Nucleic Acids Res. 37 (Database issue) D820-D823. Doi: 10.1093/nar/gkn593.


14. Sunil Sagar, Mandeep Kaur, Adam Dawe, Sundararajan V Seshadri, Alan Christoffels, Ulf Schaefer, Aleksandar Radovanovic and Vladimir B Bajic (2008). DDESC: Dragon Database for exploration of sodium channels in human. BMC Genomics 9: 622-9

13. Rajini Sreenivasan, Minnie Cai, Richard Bartfai, Xingang Wang, Alan Christoffels and Laszlo Orban (2008). Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PloSONE 3(3) e1791.


12. V Bajic, S Tan, A Christoffels, C Schombach, L Lipovich, L Yang, O Hofmann, A Kruger, W Hide and C Kai (2006). Mice and Man: Their promoter properties. PLOS Genetics. 2(4) e54.

11. A Christoffels, Sydney Brenner and Byrappa Venkatesh (2006). Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage. Comparative Biochemistry and Physiology Part D. 13-19.


10. The FANTOM Consortium, P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels et al. (2005). The Transcriptional Landscape of the Mammalian Genome. Science 309:1559-1563.

9. L Yang, J Chia, R Bartfai, A Christoffels, G.H Yue, K Ding, M.Y Ho, J. Hill, E Stupka and L Orban (2004). Analysis of the adult gonad transcriptomes in zebrafish by combining experimental and computational tools. Comparative and Functional Genomics 5: 403-418.

8. Y.H Loh, A. Christoffels, S Brenner, W Hunziker and B Venkatesh (2004). Extensive expansion of the claudin gene family in the teleost fish, Fugu. Genome Research 14(7): 1248-57.

7. A Christoffels, J Chia, E Koh, S Aparicio, S Brenner and B Venkatesh (2004). Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Molecular Biology Evolution. 21(6): 1146-1151.


6. J Kelso, J Visagie, G Theiler, A Christoffels, S Bardien, D Smedley, D Otgaar, G Greyling, C. V Jongeneel, M I. McCarthy, T Hide, W Hide (2003). EVOC: A Controlled Vocabulary for Unifying Gene Expression Data. Genome Research 13:1222-1230.

5. E Koh, K Lam, A Christoffels, M Erdman, S Brenner and B Venkatesh (2003). Hox gene clusters in the Indonesian coelacanth Latimeria menadoensis. Proceedings of the National Academy of Science. 100: 1084-1088.


4. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, H IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D and Brenner S. (2002). The sequence, assembly and analysis of the compact vertebrate genome of Fugu rubripes. Science 297 1301-1310, USA.

3. J E. Carpenter, A Christoffels, Y Weinbach, W A. Hide (2002). Assessment of the Parallelisation approach of d2-cluster for High-Performance Sequence Clustering. Journal of Computational Chemistry. UK 23(7): 755-757.


2. A Christoffels, A van Gelder, G Greyling, R Miller, T Hide and W Hide (2001). STACKdb: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Research 29(1): 234-238.


1. R. T. Miller, A. G. Christoffels, C. Gopalakrishnan, J. A. Burke, A. A. Ptitsyn, T. R. Broveak and W. A. Hide (1999). A comprehensive approach to clustering of expressed human gene structure: The Sequence Tag Alignment and Consensus Knowledgebase. Genome Research 9(11): 1143-1155.